Logic setting for simultaneous docking of multiple ligands

[Tang-Rich]

Hello, I am using Vina version 1.2.5 to process docking of multiple phenolic acid compounds and enzymes. I have encountered the following problems and would appreciate answers!

1. both active site 1 and site 2 can be docked by a single ligand. in this case of docking, how to determine the docking priority of the ligand at a single site?
2. does this docking process define the receptor as a rigid receptor, or a semi-flexible receptor?
3. Whether the binding energy of multiple ligands docked at the same time is related to the order in which the ligands are added, i.e., the order of the ligands in conf.txt.

[rwxayheee]

Hi @Tang-Rich

1.单个配体均可对接活性位点1和位点2。在这种情况下对接，如何判定配体在单个位点的对接优先性？

To determine which binding site is preferred, you could compare the docking scores at the two binding sites. But if the difference is small, then you might want to consider free energy calculation and other methods with better precision for a better estimate

2.此对接过程是把受体定义为刚性受体吗，还是半柔性受体？

By default the receptor is fully rigid. But it's possible to specify flexible sidechains. Please see: https://autodock-vina.readthedocs.io/en/latest/docking_flexible.html

3.多个配体同时对接的结合能是否与配体加入的顺序有关，即conf.txt中配体的顺序。

The order shouldn't matter. However, if you observe any order-dependent behaviors in the results (scores, poses), please let us know and we will take a look ^^